Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Koxy:BWI76_RS10695 Length = 495 Score = 588 bits (1517), Expect = e-172 Identities = 295/491 (60%), Positives = 364/491 (74%), Gaps = 4/491 (0%) Query: 7 ADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENA 66 A W+Q+A++L IE R FINGEY+ A F + P + LA+VA AD +RAV+ A Sbjct: 7 AYWQQKARELTIETRLFINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVDRAVQAA 66 Query: 67 RATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQ 126 R F+ G WSQ +PA+RKA L +FADL+ + EELALLETLD GKPI S DIPGAA+ Sbjct: 67 RGVFDRGDWSQASPAQRKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDDIPGAAR 126 Query: 127 AIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGN 186 AI W AEAIDKVY EVAPT ++L ++ REP+GV+ A+VPWNFPLL+ACWKLGPALA+GN Sbjct: 127 AIRWYAEAIDKVYGEVAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGPALASGN 186 Query: 187 SVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246 SVVLKPSEKSPLTA+R+A LA +AG+P GV NV+ G+GH G+ALALH DV+ + FTGST Sbjct: 187 SVVLKPSEKSPLTALRLAGLAKQAGLPDGVFNVVSGFGHEAGQALALHPDVEVITFTGST 246 Query: 247 KIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGS 306 + AKQL+ AG+SNMKR+WLEAGGKS NIVFAD PDLQ A A A I +NQG+VC AG+ Sbjct: 247 RTAKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQVCIAGT 306 Query: 307 RLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAK 366 RLL+E SI D+FL ++ E KGW+PGNPLDP TT+G L+D ++V S+I AG Sbjct: 307 RLLLEESIADRFLDLLKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAGEAHSTL 366 Query: 367 LLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTP 426 LL G K G PTIF V A ++QEEIFGPVL V F E+A+A+AND+ Sbjct: 367 LLDGRKNPWPAAVG----PTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALANDSR 422 Query: 427 YGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEK 486 YGL A +WT D+S+AH+ +R ++AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHALEK Sbjct: 423 YGLGAAVWTRDLSRAHRVSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEK 482 Query: 487 YTELKATWIKL 497 +TELK WI L Sbjct: 483 FTELKTIWIAL 493 Lambda K H 0.316 0.132 0.390 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 689 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 497 Length of database: 495 Length adjustment: 34 Effective length of query: 463 Effective length of database: 461 Effective search space: 213443 Effective search space used: 213443 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory